diff --git a/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala index cd4a158c1456c94656da9c770648a9b3209f0a26..e7df3db171cbba466fe7722f9af5aa288993e162 100644 --- a/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala +++ b/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet/pipelines.mypipeline +package nl.lumc.sasc.biopet.pipelines.mypipeline import nl.lumc.sasc.biopet.core.PipelineCommand import nl.lumc.sasc.biopet.core.summary.SummaryQScript @@ -29,10 +29,8 @@ class HelloPipeline(val root: Configurable) extends QScript with SummaryQScript val fastqc = new Fastqc(this) fastqc.fastqfile = config("fastqc_input") - fastqc.output = new File(outputDir, - - /* Only required when using [[SummaryQScript]] */ - addSummaryQScript(shiva) + fastqc.output = new File(outputDir, "fastqc.txt") + add(fastqc) // From here you can use the output files of shiva as input file of other jobs }